Schedule

The course meets Mondays 9:30-10:30 AM, Wednesdays 10-11 AM, and Fridays 10-11 AM or 11 AM-noon, depending on your section. All times are PST.

All course meetings are via Zoom at this link. If you miss a lecture or otherwise want to review it, lecture recordings are posted here.


The due dates, paper selections, and schedule below are tentative and subject to change.

Due dates

W 01/20
Homework 1 (based on Goentoro and Kirschner) [solutions]
W 01/20
Finalize paper choice for presentation 1 [suggested papers]
W 01/27
Homework 2 (based on Stapornwongkul, et al.) [solutions]
W 02/10
Homework 3 (based on Soroldoni, et al.) [solutions]
M 02/22
Finalize paper choice for presentation 2 [suggested papers]
W 02/24
Homework 4 (based on He, et al.) [solutions]
Tu 03/16
Homework 5 (based on Mayer, et al.) [solutions to be posted]
Tu 03/16
Homework 6 (based on Gross, et al.) due at 5 pm. [solutions to be posted]
Tu 03/16
Homework 7 due at 5 pm.

Lecture/reading/presentation schedule

Below is the class schedule. Friday class meetings typically involve discussions of research papers. Reading memos for each paper are due at 5 pm the day before the in-class discussion. The paper to be discussed is linked on the schedule. Underneath discussion papers are supplemental reading that will help give context and understanding to the main paper for our discussion. These supplemental readings are recommended, but not required.


Lecture notes download (last updated December 31, 2020)


M 01/04
1. Welcome
W 01/06
2. Biochemical kinetics in signaling
F 01/08
3. Wnt signaling (Jupyter notebook)
M 01/11
4. Reaction-diffusion patterns
W 01/13
5. The Delta-Notch system
F 01/15
Discussion of Goentoro and Kirschner paper (questions to consider)
M 01/18
No class: Martin Luther King Day
W 01/20
6. Segmentation clocks
F 01/22
Discussion of Stapornwongkul, et al. paper (questions to consider)
M 01/25
7. Effective presentations I: talk structure and delivery [slides]
W 01/27
8. Effective presentations II: slide design [slides] (talk by Jean-luc Doumont)
F 01/29
Discussion of Soroldoni, et al. paper (questions to consider)
M 02/01
Guest lecture by Sundar Naganathan
W 02/03
Student presentations
F 02/05
Student presentations
M 02/08
9. Continuum mechanics I: Conservation of mass
W 02/10
10. Continuum mechanics II: Conservation of momentum
F 02/12
11. Viscous flow in development
M 02/15
No class: Presidents Day
W 02/17
12. Continuum mechanics III: Active nematic gels (see also Jülicher, Grill, and Salbreux, 2018)
F 02/19
Discussion of He, et al. paper (questions to consider)
M 02/22
13. Viscoelasticity and laser ablation
W 02/24
Catch-up day (previous five lectures take six hours)
F 02/26
Discussion of Mayer, et al. (questions to consider)
M 03/01
Discussion of Goehring, et al. (questions to consider)
W 03/03
Course wrap-up
F 03/05
Inteview about Gross, et al. paper (questions to consider; no reading memo required)
M 03/08
Guest lecture by Peter Gross
W 03/10
Student presentations
F 03/12
Student presentations